Originally published : Wed, August 4, 2021 @ 5:16 AM
Updated : Wed, August 4, 2021 @ 9:34 PM
A common mistake when initiating an agrigenomics project is failing to consider specific sample composition before attempting DNA extraction. The composition of plant samples is highly variable, and one specific component can have a large negative impact on the quality of your extraction. This may be more complex than you think, as seeds from the same species are often so variably composed that a uniform protocol is not efficacious. Some of the most common variabilities include starch and oil concentration, along with the presence of specific enzyme inhibitors, and researchers need to be aware of variabilities within one plant. While you cannot always predict exactly what challenging components will be present, the need to troubleshoot and account for them during extraction and purification cannot be overlooked. But don’t let this overwhelm you - with the right tools and support, getting the right type of data for your downstream applications is possible.
Let’s face it - it can be challenging to extract high-quality DNA from plant samples. There are simple solutions to successfully remove common contaminants such as starch. Our custom protocols include processing steps to achieve cleaner samples; this can be as simple as additional centrifugation or using debris capture beads (non-magnetic beads) during lysis. The benefit of better quality DNA extracted for downstream applications far outweighs the additional time needed to include these important steps.
Oil-rich samples can also cause extraction challenges. Instead of resorting to expensive enzymatic cocktails that might cause additional problems downstream, LGC, Biosearch Technologies' standard lysis buffer can be successfully used for seed samples rich in oil (for example, canola oil). This buffer is part of the standard automated protocol, allowing for high-throughput processing despite the initial oil content of various samples.
Specific enzyme inhibitors (for example, kinase polymerase, ligase) can also pose a challenge for DNA extraction. Make sure that you select a kit that can provide resistance to inhibitors but is still cost-effective and doesn’t introduce new contaminants and unnecessary complexity. Failing to remove inhibitors during purification can negatively affect your library preparation with lower complexity and lower yield.
Finally, each plant will have intrinsic variability in its composition, and care must be taken to consistently sample from a specific part of a plant. Researchers should also be mindful that cell division will vary throughout the lifetime of a plant, meaning aged plant samples will require more starting material to obtain the same quantity of DNA as young plant samples.
Even after addressing the factors mentioned above, a level of unpredictability in sample composition still remains. For example, with samples that contain unusually high levels of polyphenols or unidentified inhibitors, you might need to pursue a pilot study to optimise extraction conditions before attempting high-throughput sample processing. Our team of experts is ready to help you troubleshoot these problems with technical expertise and extensive customer resources. This support includes a toolbox of different lysis and binding buffers for optimised sample component removal, allowing you to be more confident in your next generation sequencing (NGS) data.
Variable sample composition is a common problem in the field of agrigenomics. You must account for these variations in extraction and purification protocols to obtain the highest quality DNA for downstream processing. Some components like high starch and oil concentrations or the presence of specific inhibitors can be easily removed using one of our nucleic acid purification kits. However, sometimes determining what your contaminants are and how to remove them can be incredibly challenging, and DNA extraction experts can help you design and execute a pilot study for protocol optimisation. Set your NGS data up for success with custom extraction protocols built to accommodate sample composition. Learn more about how to optimise DNA purification for your sample type and downstream applications.
Or check out our extraction or purification kits and services for animal and plant DNA.